Complex simulation workflows in containerized high-performance environment

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VIŠŇOVSKÝ Vladimír SPIŠAKOVÁ Viktória HOZZOVÁ Jana OĽHA Jaroslav TRAPL Dalibor SPIWOK Vojtěch HEJTMÁNEK Lukáš KŘENEK Aleš

Rok publikování 2021
Druh Článek ve sborníku
Konference Proc. ESM 2021
Fakulta / Pracoviště MU

Ústav výpočetní techniky

Citace
Klíčová slova Docker; Jupyter notebook; Kubernetes; Molecular force field; Protein folding; Reproducibility; Workflow
Popis utting-edge research involving in-silico simulations often requires to use many heterogeneous software tools made by different developers, resulting in complex, custom-made pipelines of various scripts and programs. Such pipelines are nearly impossible to be reproduced by other research groups, jeopardizing both quality and acceptance of such research results. Starting with two in-house use cases in computational chemistry, we identified a common pattern applicable for other applications as well, and we designed and implemented a solution based on Jupyter notebooks to drive the simulation, Docker containers to package all software dependencies, and Kubernetes execution environment to run several cooperating containers which build up the whole application.
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